Tropical cyclones periodically cross the Great Barrier Reef (GBR). Physical damage from the large waves they generate can significantly alter coral reef community structure over time. Yet cyclone disturbance of the GBR has not yet been examined for more than a few events and for only part of the region. Meteorological models can be used to hindcast the likely magnitude and distribution of cyclone energy from the Australian Bureau of Meteorology's tropical cyclone database. This hindcast energy, along with measures of the spatial patterning of reefs, can be linked statistically to field observations of reef impact to predict the distribution of cyclone impacts on areas not surveyed. Implementing the requisite meteorological and spatial models within a GIS has made it feasible to apply these techniques over a longer time period (3 decades) and across a larger area (the entire GBR) than has been done before. The resultant cyclone history can be used to examine the degree to which broad measures of current reef community structure (dominant size classes and growth forms) can be explained by cyclone disturbance alone. This paper will demonstrate these modelling techniques using cyclone Joy (1990) as a case study.